Genomic Breeding of Rice

Co-Authored with Hawi Adede, a Genetic Scientist at The Africa Genomics Center & Consultancy.

Usually, coming up with a blog post is pretty much a straight-forward affair. I normally have a particular topic in mind, following some preliminary research. I also often have a narrative through which I want to communicate the message, in a creative manner. With these at hand, I sit at my desk, and just start typing.

The first thing that comes to mind creates the whole vibe for the article, and I flow with it. This very thing that allows me to create is also the barrier that has stopped me from writing this particular article sooner. I initially envisioned it in early October. And hoped to be done with it in a matter of hours.

However, there were so many vibes to flow with. When I started writing it, I realized that there were several back stories relating to rice that I needed to offload first. I also felt that I was not knowledgeable enough about the topic, and needed to read some more.

So, I put this one aside as a very sketchy draft and worked on the others as I gathered more information. On 1st October, I started with a philosophical, introspective one on the nature of change. I concluded that flow with one on the genetic diversity of rice, particular the Indian strains- on 29th November.

These several weeks later, the one on genomic breeding of rice is finally ready. I co-wrote it with Hawi Adede, a Geneticist. She added valuable input and allowed me to have a better understanding of genetics, and how vast the field is. Today, though, we will just focus on how it can be used to feed a hungry planet.

In September, I started pursuing a 7-week course on "Feeding a Hungry Planet" by the SDG Academy on EDX. As it is a self-paced program, I am yet to complete it. My pace is guided by the ability to generate articles from whatever I learn.

These articles as to share it with my readers. This is the latest of those articles, and I will soon go back to the course work. So far, however, I have concentrated my writing on one particular item in the course material: Rice.

As the most widely consumed food crop in the world, rice takes a center stage in the program. According to the tutors, rice production has to increase significantly to meet the steeply rising demand. This has to be done with minimal environmental impacts, despite the harsher climate.

To achieve this, they call for sustainable intensification of rice farming. That requires a multi-sectoral approach so as to allow for sustainable production to feed the planet. As illustrated in this screen-grab from the program, one of the major components is genetic intensification.

In this context, intensification describes the process of enhancing the performance of agricultural resources. One such natural capital is biodiversity. Therefore, genetic intensification of rice refers to the process of improving the productivity of rice by tapping into its biodiversity. This can be done through genomic breeding approaches.

Why Rice is Ripe for Genomic Breeding

According to this article, domesticated rices are classified under the genus Oryzas. There are dozens of rice species therein, with each having a unique genetic composition. Therefore, there is a great diversity in attributes such as color, panicle length, lodging resistance, flowering time, and aroma.

Such variations present crop scientists with a rich reservoir of genes which they can tap into for intensification of the rice plant. These genes can be exploited in rice breeding programs. International teams of scientists are currently taking such steps with the intention of breeding a set of sustainable crops known as the green super rice.

Other than this diversity, there are two other factors which make rice a suitable candidate for genomic breeding. One of these is that the rice diploid rice genome is the smallest among all domesticated cereals (400 MBs) and therefore can be easily studied.

The second one is the fact that rice is the first crop whose genome has been completely sequenced. As of 2017, around 3000 of its genes had been analyzed for biological functions. These can be classified into relevant categories based on the needs of the breeding program.

How Conventional Breeding is Done

Before delving deeper into genomic breeding, it is important to first highlight how conventional/traditional crop breeding is done. In a nutshell, it goes like this: A breeder may identify a crop with high yields but low disease resistance. The breeder may then identify another crop with high disease resistance but which produces lower yields.

The two are cross-pollinated to produce seeds which are then grown into the desirable hybrid cultivars. The hybrid contains the both characteristics- disease resistance and high yields. These hybrids may be back-crossed severally till a certain target is achieved. This is usually a lengthy process as each cultivar has to grow to maturity. It can also be inaccurate as some undesirable traits may accidentally be introduced into the hybrid.

How Genomic Breeding is Done

Genomic breeding heavily relies on the data, knowledge, tools, and technology developed through genetic studies on not only rice but also other plants. These resources are utilized in the identification, selection, and transfer of genes which code for beneficial agronomic traits.

That is done via subtle genetic modifications which maintain biodiversity rather than encouraging one best strain as is often the case with conventional breeding. It is also a faster process as the cultivars do not have to be grown to maturity. Additionally, it is a precise operation as there is no accidental introgression of unwanted genes.

There are two genomic breeding techniques:

1. Genomic design

This involves designing a plant from scratch by listing a set of desirable traits. These may include ability to grow in, for instance, dry areas, and cooking characteristics such as the aroma. This is followed by genome-wide association studies (GWAS) to identify the genes associated with those listed traits.

Afterwards, germplasm containing these target genes are identified and strategies for assembling them defined. Assembling involves bringing together these target genes in a single cultivar, which is the desired breed.  

2. Whole-genome selection

This method relies on DNA marker tools for identifying and selecting particular genes in the entire rice genome. Since genetic markers are molecules of known location, the genes therein can be modified once identified. This is referred to as Marker Assisted Selection (MAS) or molecular breeding.

The breeding process starts by deciding the segments of DNA which are to be modified. For instance, these may be the genes for flowering time or those for grain length. Thereafter, the markers flanking each gene are identified and the genes modified accordingly. The resulting cultivar will exhibit the characteristics it has been modified for.

Gene Banks 

Both genetic information and germplasm (plant material) neede in genomic breeding programs. These can be obtained in one or more of the rice gene banks found around the world. These include the International Rice Research Institute in the Philippines (130,000 accessions, 4000+ being wild varieties); Oryzabase in Japan (22,000 accessions), and the Africa Rice Genebank in the Ivory Coast (20,000 accessions).

The Gramene database also contains genomic information for both cultivated and wild rice accessions, among other plants. This includes data on grain length and panicle architecture from 1500+ rice varieties. Coupled with a variety of analytical tools, it allows researchers to compare and download this information for use in breeding programs.

There are ongoing efforts to establish a global, public rice genetic database which would advance breeding technologies for future rice improvement. In 2014, consortium consisting of the International Rice Research Institute, Beijing Genomic Institute, and the Chinese Academy of Science embarked on the 3000 Rice Genomes Project. 

This project involved re-sequencing 3000 rice accessions from 89 countries. using a variety of advanced genetic and bioinformatic techniques, they dug deeper into the rice genome to understand its diversity and the genes associated with important phenotypes (attributes). The dataset from this project is publicly available and serves as the foundation for a global rice genetic database.

Attributes Selected for through Genomic Breeding

All breeding programs are designed to select a set of desirable attributes. The journal article this post is based on speaks of five particular characteristics that are vital in the genomic breeding of Green Super Rice. In the next post, we will explain how these crops with these characteristics are bred:

1. Resistance to pests and diseases
2. Efficient nutrient use
3. Improved yield
4. Resistance to abiotic stress
5. Enhanced grain quality.